hi Pankaj,

You should follow the multifactor analysis section of the vignette. You
would include the patient effect in the design like so:

design(dds) <- ~ patient + condition

Where 'patient' and 'condition' are factors which are columns in
colData(dds), and condition has levels: normal, tumor (where normal is the
base level).

Then results(dds) will build a result table for tumor vs normal,
controlling for the patient effect.

Mike


On Thu, Apr 10, 2014 at 3:52 PM, Pankaj Agarwal <p.agarwal@duke.edu> wrote:

> Hi,
>
> This query is in reference to the following post
> https://stat.ethz.ch/pipermail/bioconductor/2010-April/032869.html
> where it was mentioned that "DESeq does not support paired tests  (yet)".
>  I have a need for performing rna-seq data analysis with matched
> tumor/normal pairs of data and was wondering if this capability is now
> available in the latest version of DESeq2.  I searched the list site and
> also the latest vignette, but could not find anything indicating this
> capability is now available in DEseq.  I would be grateful if, in case this
> feature is not yet available, someone could advice me how to do the
> analysis.  I have samples from two patients, and from each patient there is
> a "normal" and a "tumor" rna-seq sample data.
>
> Thanks,
>
> - Pankaj
>
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